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Cloufield / gwaslab

A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
GNU General Public License v3.0
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Outdated urls? #111

Closed Sandyyy123 closed 1 month ago

Sandyyy123 commented 1 month ago

Hello Mr. Cloudfield,

I am having this error, it seems URL has changed to https://hgdownload.soe.ucsc.edu/gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz. I am unable to locate the file where I can change the url. Please help.

mysumstats.liftover(n_cores=20, to_build="38") 2024/10/24 20:27:52 Start to perform liftover...v3.4.46 2024/10/24 20:27:52 -Current Dataframe shape : 7137570 x 11 ; Memory usage: 504.57 MB 2024/10/24 20:27:52 -Number of threads/cores to use: 20 2024/10/24 20:27:52 -Creating converter : hg19 to hg38 2024/10/24 20:27:53 -Converting variants with status code xxx0xxx :7137570... WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f3769dcb490>: Failed to establish a new connection: [Errno 110] Connection timed out')': /goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz

I also had a similar issue downloading gtf file. Changing the website for downloading gtf file here (Required for gene annotation) in reference.json file worked. ensembl_hg19_gtf = https://ftp.ensembl.org/pub/grch37/release-113/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.chr.gtf.gz

Sandyyy123 commented 1 month ago

Matter got fixed using the latest version 3.4.49